Targeted base editing in the plastid genome of Arabidopsis thaliana.
Journal
Nature plants
ISSN: 2055-0278
Titre abrégé: Nat Plants
Pays: England
ID NLM: 101651677
Informations de publication
Date de publication:
07 2021
07 2021
Historique:
received:
09
01
2021
accepted:
26
05
2021
pubmed:
3
7
2021
medline:
24
9
2021
entrez:
2
7
2021
Statut:
ppublish
Résumé
Bacterial cytidine deaminase fused to the DNA binding domains of transcription activator-like effector nucleases was recently reported to transiently substitute a targeted C to a T in mitochondrial DNA of mammalian cultured cells
Identifiants
pubmed: 34211131
doi: 10.1038/s41477-021-00954-6
pii: 10.1038/s41477-021-00954-6
pmc: PMC8289735
doi:
Substances chimiques
Chlorophyll
1406-65-1
Types de publication
Comparative Study
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
906-913Informations de copyright
© 2021. The Author(s).
Références
Mok, B. Y. et al. A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing. Nature 583, 631–637 (2020).
doi: 10.1038/s41586-020-2477-4
Piatek, A. A., Lenaghan, S. C. & Stewart, C. N. Advanced editing of the nuclear and plastid genomes in plants. Plant Sci. 273, 42–49 (2018).
doi: 10.1016/j.plantsci.2018.02.025
Yu, Q., Lutz, K. A. & Maliga, P. Efficient plastid transformation in Arabidopsis. Plant Physiol. 175, 186–193 (2017).
doi: 10.1104/pp.17.00857
Ruf, S. et al. High-efficiency generation of fertile transplastomic Arabidopsis plants. Nat. Plants 5, 282–289 (2019).
doi: 10.1038/s41477-019-0359-2
Fuentes, P., Armarego-Marriott, T. & Bock, R. Plastid transformation and its application in metabolic engineering. Curr. Opin. Biotechnol. 49, 10–15 (2018).
doi: 10.1016/j.copbio.2017.07.004
Sakuma, T. et al. Repeating pattern of non-RVD variations in DNA-binding modules enhances TALEN activity. Sci. Rep. 3, 3379 (2013).
Cerutti, H., Osman, M., Grandoni, P. & Jagendorf, A. T. A homolog of Escherichia coli RecA protein in plastids of higher plants. Proc. Natl Acad. Sci. USA 89, 8068–8072 (1992).
doi: 10.1073/pnas.89.17.8068
Cao, J., Combs, C. & Jagendorf, A. T. The chloroplast-located homolog of bacterial DNA recombinase. Plant Cell Physiol. 38, 1319–1325 (1997).
doi: 10.1093/oxfordjournals.pcp.a029124
Mol, C. D. et al. Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: protein mimicry of DNA. Cell 82, 701–708 (1995).
doi: 10.1016/0092-8674(95)90467-0
Arimura, S. et al. Targeted gene disruption of ATP synthases 6-1 and 6-2 in the mitochondrial genome of Arabidopsis thaliana by mitoTALENs. Plant J. 104, 1459–1471 (2020).
doi: 10.1111/tpj.15041
Kazama, T. et al. Curing cytoplasmic male sterility via TALEN-mediated mitochondrial genome editing. Nat. Plants 5, 722–730 (2019).
doi: 10.1038/s41477-019-0459-z
Clough, S. J. & Bent, A. F. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735–743 (1998).
doi: 10.1046/j.1365-313x.1998.00343.x
Miyazaki, K. & Kitahara, K. Functional metagenomic approach to identify overlooked antibiotic resistance mutations in bacterial rRNA. Sci. Rep. 8, 5179 (2018).
D’Costa, V. M., McGrann, K. M., Hughes, D. W. & Wright, G. D. Sampling the antibiotic resistome. Science 311, 374–377 (2006).
doi: 10.1126/science.1120800
Allison, L. A., Simon, L. D. & Maliga, P. Deletion of rpoB reveals a second distinct transcription system in plastids of higher plants. EMBO J. 15, 2802–2809 (1996).
doi: 10.1002/j.1460-2075.1996.tb00640.x
Chateigner-Boutin, A.-L. et al. OTP70 is a pentatricopeptide repeat protein of the E subgroup involved in splicing of the plastid transcript rpoC1. Plant J. 65, 532–542 (2011).
doi: 10.1111/j.1365-313X.2010.04441.x
Baena-González, E. et al. Deletion of the tobacco plastid psbA gene triggers an upregulation of the thylakoid-associated NAD(P)H dehydrogenase complex and the plastid terminal oxidase (PTOX). Plant J. 35, 704–716 (2003).
doi: 10.1046/j.1365-313X.2003.01842.x
Schult, K. et al. The nuclear-encoded factor HCF173 is involved in the initiation of translation of the psbA mRNA in Arabidopsis thaliana. Plant Cell 19, 1329–1346 (2007).
doi: 10.1105/tpc.106.042895
Lutz, K. A. & Maliga, P. Plastid genomes in a regenerating tobacco shoot derive from a small number of copies selected through a stochastic process. Plant J. 56, 975–983 (2008).
doi: 10.1111/j.1365-313X.2008.03655.x
Khakhlova, O. & Bock, R. Elimination of deleterious mutations in plastid genomes by gene conversion. Plant J. 46, 85–94 (2006).
doi: 10.1111/j.1365-313X.2006.02673.x
Weijers, D. et al. An Arabidopsis minute-like phenotype caused by a semi-dominant mutation in a RIBOSOMAL PROTEIN S5 gene. Development 128, 4289–4299 (2001).
doi: 10.1242/dev.128.21.4289
Tsutsui, H. & Higashiyama, T. pKAMA-ITACHI vectors for highly efficient CRISPR/Cas9-mediated gene knockout in Arabidopsis thaliana. Plant Cell Physiol. 58, 46–56 (2017).
doi: 10.1093/pcp/pcx098
Shimada, T. L., Shimada, T. & Hara-Nishimura, I. A rapid and non-destructive screenable marker, FAST, for identifying transformed seeds of Arabidopsis thaliana. Plant J. 61, 519–528 (2010).
doi: 10.1111/j.1365-313X.2009.04060.x
Moazed, D. & Noller, H. F. Interaction of antibiotics with functional sites in 16S ribosomal RNA. Nature 327, 389–394 (1987).
doi: 10.1038/327389a0
Svab, Z. & Maliga, P. Mutation proximal to the tRNA binding region of the Nicotiana plastid 16S rRNA confers resistance to spectinomycin. Mol. Gen. Genet. 228, 316–319 (1991).
doi: 10.1007/BF00282483
Filipenko, E. A., Sidorchuk, Y. V. & Deineko, E. V. Spontaneous spectinomycin resistance mutations of the chloroplast rrn16 gene in Daucus carota callus lines. Russian J. Genet. 47, 35–40 (2011).
doi: 10.1134/S1022795410121026
Zoschke, R. & Bock, R. Chloroplast translation: structural and functional organization, operational control, and regulation. Plant Cell 30, 745–770 (2018).
doi: 10.1105/tpc.18.00016
Lee, H. et al. Mitochondrial DNA editing in mice with DddA-TALE fusion deaminases. Nat. Commun. 12, 1190 (2021).
doi: 10.1038/s41467-021-21464-1
Zhu, A., Guo, W., Gupta, S., Fan, W. & Mower, J. P. Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates. New Phytol. 209, 1747–1756 (2016).
doi: 10.1111/nph.13743
Sikdar, S. R., Serino, G., Chaudhuri, S. & Maliga, P. Plastid transformation in Arabidopsis thaliana. Plant Cell Rep. 18, 20–24 (1998).
doi: 10.1007/s002990050525
Tan, J., Zhang, F., Karcher, D. & Bock, R. Engineering of high-precision base editors for site-specific single nucleotide replacement. Nat. Commun. 10, 439 (2019).
Orr, D. J. et al. Surveying Rubisco diversity and temperature response to improve crop photosynthetic efficiency. Plant Physiol. 172, 707–717 (2016).
pubmed: 27342312
pmcid: 5047088
Sharwood, R. E., Ghannoum, O., Kapralov, M. V., Gunn, L. H. & Whitney, S. M. Temperature responses of Rubisco from Paniceae grasses provide opportunities for improving C3 photosynthesis. Nat. Plants 2, 16186 (2016).
doi: 10.1038/nplants.2016.186
Oettmeier, W. Herbicide resistance and supersensitivity in photosystem II. Cell. Mol. Life Sci. 55, 1255–1277 (1999).
doi: 10.1007/s000180050370
Nagaya, S., Kawamura, K., Shinmyo, A. & Kato, K. The HSP terminator of Arabidopsis thaliana increases gene expression in plant cells. Plant Cell Physiol. 51, 328–332 (2010).
doi: 10.1093/pcp/pcp188
Karimi, M., Inzé, D. & Depicker, A. GATEWAY
doi: 10.1016/S1360-1385(02)02251-3
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
doi: 10.1093/bioinformatics/btp324
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
doi: 10.1093/bioinformatics/btp352
Porra, R. J., Thompson, W. A. & Kriedemann, P. E. Determination of accurate extinction coefficients and simultaneous equations for assaying chlorophylls a and b extracted with four different solvents: verification of the concentration of chlorophyll standards by atomic absorption spectroscopy. Biochim. Biophys. Acta Bioenerg. 975, 384–394 (1989).
doi: 10.1016/S0005-2728(89)80347-0